I've been using non-monospaced fonts for a long time now. I also have had no issues with things I or others have lined up. "Lining things up" usually amounts to screwing around - like variable names having identical lengths, at the expense of clarity. I actually can't think of any issues that I've had. At all. I have noticed that it's a easier to read, scan, and recognize the code. There is, after all, a reason monospaced fonts are hardly ever used elsewhere - not in technical reference manuals, dictionaries, fiction...

I usually keep my mouth shut about it because a lot of programmers identify with monospaced fonts (especially ugly ones). I suggest others do the same: quietly try it, because after the "this is different, therefore I hate it" feeling passes, you might find you prefer it.